Move OptionalComponentsPresent from newPackage to beginDocumentation

I generally don't appreciate packages that run an external program upon being loaded (which also ends up happening when `Macaulay2Doc` is being installed, c.f. #3292).

Perhaps `OptionalComponentsPresent` should be set _after_ `newPackage` in the call to `beginDocumentation`, so that loading could stop there if the optional component is not present.

(Originally from https://github.com/Macaulay2/M2/pull/3366#discussion_r1685557557)

Start by tracing the OptionalComponentsPresent handling in newPackage and beginDocumentation, and review the context from pull request #3366 and issue #3292. Determine when loading Macaulay2Doc invokes an external program and define the intended behavior when the optional component is absent; done means package loading no longer triggers that work prematurely.

Written by the indexing model from the issue text.